NAME
gustaf - Gustaf - Generic mUlti-SpliT Alignment Finder: Tool for split-read mapping allowing multiple splits.
SYNOPSIS
gustaf [OPTIONS] <GENOME FASTA FILE> <READ FASTA FILE>
gustaf [OPTIONS] <GENOME FASTA FILE> <READ FASTA FILE> <READ FASTA FILE 2>
DESCRIPTION
GUSTAF uses SeqAns STELLAR to find splits as local matches on different strands or chromosomes. Criteria and penalties to chain these matches can be specified. Output file contains the breakpoints along the best chain.
The genome file is used as database input, the read file as query input.
All STELLAR options are supported. See STELLAR documentation for STELLAR parameters and options.
(c) 2011-2012 by Kathrin Trappe
REQUIRED ARGUMENTS
- FASTA_FILE_1 INPUT_FILE
-
Valid filetypes are: .fq, .fastq, .fasta, and .fa.
- FASTA_FILE_2 List of INPUT_FILE's
-
Either one (single-end) or two (paired-end) read files. Valid filetypes are: .fq, .fastq, .fasta, and .fa.
OPTIONS
- -h, --help
-
Display the help message.
- --version
-
Display version information.
Main Options:
- -tp, --transPen INTEGER
-
Interchromosomal translocation penalty Default: 5.
- -ip, --invPen INTEGER
-
Inversion penalty Default: 5.
- -op, --orderPen INTEGER
-
Intrachromosomal order change penalty Default: 0.
- -oth, --overlapThresh DOUBLE
-
Allowed overlap between matches Default: 0.5.
- -gth, --gapThresh INTEGER
-
Allowed gap length between matches, default value corresponse to expected size of microindels (5 bp) Default: 5.
- -ith, --initGapThresh INTEGER
-
Allowed initial or ending gap length at begin and end of read with no breakpoint (e.g. due to sequencing errors at the end) Default: 15.
- -bth, --breakendThresh INTEGER
-
Allowed initial or ending gap length at begin and end of read that creates a breakend/breakpoint (e.g. for reads extending into insertions) Default: 30.
- -tth, --tandemThresh INTEGER
-
Minimal length of (small) insertion/duplication with double overlap to be considered tandem repeat Default: 50.
- -pth, --breakpoint-pos-range INTEGER
-
Allowed difference in breakpoint position Default: 5.
- -cbp, --complex-breakpoints
-
Disable inferring complex SVs
- -st, --support INTEGER
-
Number of supporting reads Default: 2.
- -mst, --mate-support INTEGER
-
Number of supporting concordant mates Default: 2.
- -ll, --library-size INTEGER
-
Library size of paired-end reads
- -le, --library-error INTEGER
-
Library error (sd) of paired-end reads
- -rc, --revcompl
-
Disable reverse complementing second mate pair input file.
Input Options:
- -m, --matchfile INPUT_FILE
-
File of (stellar) matches Valid filetypes are: .gff and .GFF.
Output Options:
- -gff, --gffOut OUTPUT_FILE
-
Name of gff breakpoint output file. Valid filetypes are: .txt and .gff. Default: breakpoints.gff.
- -vcf, --vcfOut OUTPUT_FILE
-
Name of vcf breakpoint output file. Valid filetypes are: .vcf and .txt. Default: breakpoints.vcf.
- -j, --jobName STRING
-
Job/Queue name Default: .
- -do, --dots
-
Enable graph output in dot format
Parallelization Options:
- -nth, --numThreads INTEGER
-
Number of threads for parallelization of I/O. Default: 1.
Main Options:
- -e, --epsilon DOUBLE
-
Maximal error rate (max 0.25). In range [0.0000001..0.25]. Default: 0.05.
- -l, --minLength INTEGER
-
Minimal length of epsilon-matches. In range [0..inf]. Default: 100.
- -f, --forward
-
Search only in forward strand of database.
- -r, --reverse
-
Search only in reverse complement of database.
- -a, --alphabet STRING
-
Alphabet type of input sequences (dna, rna, dna5, rna5, protein, char). One of dna, dna5, rna, rna5, protein, and char.
- -v, --verbose
-
Set verbosity mode.
Filtering Options:
- -k, --kmer INTEGER
-
Length of the q-grams (max 32). In range [1..32].
- -rp, --repeatPeriod INTEGER
-
Maximal period of low complexity repeats to be filtered. Default: 1.
- -rl, --repeatLength INTEGER
-
Minimal length of low complexity repeats to be filtered. Default: 1000.
- -c, --abundanceCut DOUBLE
-
k-mer overabundance cut ratio. In range [0..1]. Default: 1.
Verification Options:
- -x, --xDrop DOUBLE
-
Maximal x-drop for extension. Default: 5.
- -vs, --verification STRING
-
Verification strategy: exact or bestLocal or bandedGlobal One of exact, bestLocal, and bandedGlobal. Default: exact.
- -dt, --disableThresh INTEGER
-
Maximal number of verified matches before disabling verification for one query sequence (default infinity). In range [0..inf].
- -n, --numMatches INTEGER
-
Maximal number of kept matches per query and database. If STELLAR finds more matches, only the longest ones are kept. Default: 50.
- -s, --sortThresh INTEGER
-
Number of matches triggering removal of duplicates. Choose a smaller value for saving space. Default: 500.